6:26 p.m.
details: http://www.bx.psu.edu/hg/galaxy/rev/40f58d95a051
changeset: 2778:40f58d95a051
user: Anton Nekrutenko <anton(a)bx.psu.edu>
date: Fri Sep 25 13:58:15 2009 -0400
description:
Added Cite to masthead
5 file(s) affected in this change:
templates/base_panels.mako
tools/fastx_toolkit/fastq_to_fasta.xml
tools/samtools/pileup_parser.xml
tools/samtools/sam_pileup.xml
universe_wsgi.ini.sample
diffs (80 lines):
diff -r 6a86a558f405 -r 40f58d95a051 templates/base_panels.mako
--- a/templates/base_panels.mako Fri Sep 25 11:32:47 2009 -0400
+++ b/templates/base_panels.mako Fri Sep 25 13:58:15 2009 -0400
@@ -167,11 +167,16 @@
<div class="submenu">
<ul>
<li><a href="${app.config.get( "bugs_email",
"mailto:galaxy-bugs@bx.psu.edu" )}">Email comments, bug reports, or
suggestions</a></li>
- <li><a target="_blank" href="${app.config.get(
"wiki_url", "http://g2.trac.bx.psu.edu/" )}">Galaxy
Wiki</a></li>
- <li><a target="_blank" href="${app.config.get(
"screencasts_url", "http://g2.trac.bx.psu.edu/wiki/ScreenCasts"
)}">Video tutorials (screencasts)</a></li>
+ <li><a target="_blank" href="${app.config.get(
"wiki_url", "http://bitbucket.org/galaxy/galaxy-central/wiki"
)}">Galaxy Wiki</a></li>
+ <li><a target="_blank" href="${app.config.get(
"screencasts_url", "http://galaxycast.org" )}">Video tutorials
(screencasts)</a></li>
</ul>
</div>
</td>
+
+ <td class="tab">
+ <a target="_blank" href="${app.config.get(
"citation_url",
"http://bitbucket.org/galaxy/galaxy-central/wiki/Citations"
)}">Cite</a>
+ </td>
+
<td class="tab">
<a>User</a>
@@ -282,7 +287,7 @@
</head>
<body scroll="no" class="${self.body_class}">
- <div id="everything" style="position: absolute; top: 0; left: 0;
width: 100%; height: 100%; min-width: 600px;">
+ <div id="everything" style="position: absolute; top: 0; left: 0;
width: 100%; height: 100%; min-width: 960px;">
## Background displays first
<div id="background"></div>
## Layer iframes over backgrounds
diff -r 6a86a558f405 -r 40f58d95a051 tools/fastx_toolkit/fastq_to_fasta.xml
--- a/tools/fastx_toolkit/fastq_to_fasta.xml Fri Sep 25 11:32:47 2009 -0400
+++ b/tools/fastx_toolkit/fastq_to_fasta.xml Fri Sep 25 13:58:15 2009 -0400
@@ -3,7 +3,7 @@
<command>gunzip -cf $input | fastq_to_fasta $SKIPN $RENAMESEQ -o $output -v
</command>
<inputs>
- <param format="fastqsolexa" name="input" type="data"
label="FASTQ Library to convert" />
+ <param format="fastqsolexa,fastqsanger" name="input"
type="data" label="FASTQ Library to convert" />
<param name="SKIPN" type="select" label="Discard sequences
with unknown (N) bases ">
<option value="">yes</option>
diff -r 6a86a558f405 -r 40f58d95a051 tools/samtools/pileup_parser.xml
--- a/tools/samtools/pileup_parser.xml Fri Sep 25 11:32:47 2009 -0400
+++ b/tools/samtools/pileup_parser.xml Fri Sep 25 13:58:15 2009 -0400
@@ -1,5 +1,5 @@
-<tool id="pileup_parser" name="Parse pileup">
- <description>to find variants</description>
+<tool id="pileup_parser" name="Filter pileup">
+ <description>on coverage and SNPs</description>
<command interpreter="perl">
#if $pileup_type.type_select == "six": #pileup_parser.pl $input
"3" "5" "6" "4" $qv_cutoff $cvrg_cutoff $snps_only
$interval "2" $out_file1
#elif $pileup_type.type_select == "ten": #pileup_parser.pl $input
"3" "9" "10" "8" $qv_cutoff $cvrg_cutoff
$snps_only $interval "2" $out_file1
diff -r 6a86a558f405 -r 40f58d95a051 tools/samtools/sam_pileup.xml
--- a/tools/samtools/sam_pileup.xml Fri Sep 25 11:32:47 2009 -0400
+++ b/tools/samtools/sam_pileup.xml Fri Sep 25 13:58:15 2009 -0400
@@ -1,5 +1,5 @@
-<tool id="sam_pileup" name="SAM Pileup Format"
version="1.0.0">
- <description>generates the pileup format for a provided BAM
file</description>
+<tool id="sam_pileup" name="Generate pileup"
version="1.0.0">
+ <description>from BAM dataset</description>
<command interpreter="python">
sam_pileup.py
--input1=$input1
diff -r 6a86a558f405 -r 40f58d95a051 universe_wsgi.ini.sample
--- a/universe_wsgi.ini.sample Fri Sep 25 11:32:47 2009 -0400
+++ b/universe_wsgi.ini.sample Fri Sep 25 13:58:15 2009 -0400
@@ -102,9 +102,11 @@
## Brand: appends "/[brand]" to the "Galaxy" text in the masthead
## wiki_url: replaces the default galaxy main wiki
## bugs_email: replaces the default galaxy bugs email list
+##citation_url: point to a URL listing citations
#brand = Private local mirror
#wiki_url = /path/to/my/local/wiki
#bugs_email = mailto:galaxy-bugs@example.org
+#citation_url = /path/to/my/citations
# ---- Logging and Debugging ------------------------------------------------
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